Fish biodiversity in Marine World Heritage Sites

library(sf)
library(dplyr)

if (!file.exists("shape/worldheritagemarineprogramme.shp")) {
  download.file("http://geo.vliz.be/geoserver/wfs?request=getfeature&service=wfs&version=1.0.0&typename=MarineRegions:worldheritagemarineprogramme&outputformat=SHAPE-ZIP", "shape.zip")
  unzip("shape.zip", exdir = "shape")
}

shapes <- st_read("shape/worldheritagemarineprogramme.shp") %>%
  select(full_name, country, geometry) %>%
  mutate(full_name = iconv(full_name, "latin1", "UTF-8"))

library(mapview)
mapviewOptions(fgb = FALSE)

mapview(shapes)@map

library(concaveman)
library(sfheaders)

shapes_processed <- shapes %>%
  mutate(geometry = sf_remove_holes(geometry)) %>%
  group_by(full_name) %>%
  summarize(geometry = st_union(geometry))

mapview(shapes, color = "red", lwd = 0.5, alpha = 1, alpha.regions = 0) +
  mapview(shapes_processed, color = "green", lwd = 0.5, alpha = 1, alpha.regions = 0, legend = FALSE)

library(purrr)

occ_for_geom <- function(geom) {
  wkt <- st_as_text(st_as_sfc(st_bbox(geom)), digits = 6)
  message(wkt)
  occ <- occurrence(geometry = wkt, fields = c("scientificName", "species", "family", "order", "class", "superclass", "phylum", "decimalLongitude", "decimalLatitude", "date_year", "category", "dataset_id")) %>%
    st_as_sf(coords = c("decimalLongitude", "decimalLatitude"), crs = 4326)
  occ_filtered <- occ %>%
    filter(st_intersects(geometry, geom, sparse = FALSE)) %>%
    as_tibble() %>%
    select(-geometry)
  return(occ_filtered)
}

if (!file.exists("occurrence.Rdata")) {
  occs <- map(shapes_processed$geometry, occ_for_geom)
  for (i in 1:nrow(shapes_processed)) {
    occs[[i]]$full_name <- shapes_processed$full_name[i]
  }
  occ <- bind_rows(occs)

  occ <- occ %>%
    mutate(species_fish = ifelse(superclass == "Pisces", species, NA)) %>%
    mutate(species_vulnerable = ifelse(category %in% c("VU", "EN", "CR"), species, NA)) %>%
    mutate(species_vulnerable_fish = ifelse(superclass == "Pisces" & category %in% c("VU", "EN", "CR"), species, NA))

  save(occ, file = "occurrence.Rdata")
} else {
  load("occurrence.Rdata")
}

occ %>%
  filter(!is.na(species)) %>%
  summarize(
    records = n(),
    species = length(unique(species)),
    fish = length(unique(species_fish)),
    vulnerable = length(unique(species_vulnerable)),
    vulnerable_fish = length(unique(species_vulnerable_fish))
  ) %>%
  kable(format.args = list(big.mark = ","))

occ %>%
  filter(!is.na(species)) %>%
  group_by(full_name) %>%
  summarize(
    records = n(),
    species = length(unique(species)),
    fish = length(unique(species_fish)),
    vulnerables = length(unique(species_vulnerable)),
    vulnerable_fish = length(unique(species_vulnerable_fish))
  ) %>%
  kable(format.args = list(big.mark = ","))